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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Expanding the Scope of Bacterial CRISPR Activation with PAM-Flexible dCas9 Variants

CRISPR-Cas transcriptional tools have been widely applied for programmable regulation of complex biological networks. In comparison to eukaryotic systems, bacterial CRISPR activation (CRISPRa) has stringent target site requirements for effective gene activation. While genes may not always have an NGG protospacer adjacent motif (PAM) at the appropriate position, PAM-flexible dCas9 variants can expand the range of targetable sites. Here we systematically evaluate a panel of PAM-flexible dCas9 variants for their ability to activate bacterial genes. We observe that dxCas9-NG provides a high dynamic range of gene activation for sites with NGN PAMs while dSpRY permits modest activity across almost any PAM. Similar trends were observed for heterologous and endogenous promoters. For all variants tested, improved PAM-flexibility comes with the trade-off that CRISPRi-mediated gene repression becomes less effective. Weaker CRISPR interference (CRISPRi) gene repression can be partially rescued by expressing multiple sgRNAs to target many sites in the gene of interest. Furthermore, our work provides a framework to choose the most effective dCas9 variant for a given set of gene targets, which will further expand the utility of CRISPRa/i gene regulation in bacterial systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Geometric Transformations Afforded by Rotational Freedom in Aramid Amphiphile Nanostructures

Molecular self-assembly in water leads to nanostructure geometries that can be tuned owing to the highly dynamic nature of amphiphiles. There is growing interest in strongly interacting amphiphiles with suppressed dynamics, as they exhibit ultrastability in extreme environments. However, such amphiphiles tend to assume a limited range of geometries upon self-assembly due to the specific spatial packing induced by their strong intermolecular interactions. To overcome this limitation while maintaining structural robustness, we incorporate rotational freedom into the aramid amphiphile molecular design by introducing a diacetylene moiety between two aramid units, resulting in diacetylene aramid amphiphiles (D-AAs). This design strategy enables rotations along the carbon–carbon sp hybridized bonds of an otherwise fixed aramid domain. We show that varying concentrations and equilibration temperatures of D-AA in water lead to self-assembly into four different nanoribbon geometries: short, extended, helical, and twisted nanoribbons, all while maintaining robust structure with thermodynamic stability. In conclusion, we use advanced microscopy, X-ray scattering, spectroscopic techniques, and two-dimensional (2D) NMR to understand the relationship between conformational freedom within strongly interacting amphiphiles and their self-assembly pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Impact of Coastal Marsh Eco‐Geomorphologic Change on Saltwater Intrusion Under Future Sea Level Rise

Abstract Coastal saltwater intrusion (SWI) is one key factor that affects the hydrology, ecology, and biogeochemistry of coastal ecosystems. Future climate change, especially intensified sea level rise (SLR), is expected to trigger SWI to encroach on coastal freshwater aquifers more intensively. Numerous studies have investigated decadal/century scale SWI under SLR by assuming a static coastal landscape topography. However, coastal landscapes are highly dynamic in response to SLR, and the impact of coastal landscape evolution on SWI has received very little attention. Thus, this study used a coastal marsh landscape as an example and investigated how coastal marsh evolution affects future SWI with a physically‐based coastal hydro‐eco‐geomorphologic model, Advanced Terrestrial Simulator. Our numerical experiments showed that it is very likely that the marsh elevation increases with future SLR due to sediment deposition, and a depression zone is formed due to different marsh accretion rates between the ocean boundary and the inland. We found that marsh accretion may significantly reduce the surface saltwater inflow at the ocean boundary, and the evolved topographic depression zone may prolong the residence time of surface ponded saltwater, affecting subsurface salinity distribution differently. We also predicted that marshlands may become more sensitive to upland freshwater supply under future SLR, compared with previous predictions without marsh evolution. This study demonstrates the importance of coastal evolution to coastal freshwater‐saltwater interaction. The eco‐geomorphologic effect may not be ignored when evaluating coastal SWI under SLR at decadal or century scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

First Synoptic Images of FUV Discrete Aurora and Discovery of Sinuous Aurora at Mars by EMM EMUS

Abstract We present the first measurements of Mars discrete aurora in the extreme ultraviolet (<110 nm) and the first synoptic aurora images in the far ultraviolet (110–180 nm). Auroral emission is detected in >75% of nightside images, with patterns shifting visibly over 15–20 min. Aurora is observed most frequently in regions of open magnetic topology (where crustal magnetic fields are very weak and/or vertical), with the brightest aurora where crustal fields are strongest. We present the first disk‐averaged spectrum of discrete aurora, with several O, C, and CO features as expected for electron impact primarily on CO 2 . We categorize discrete auroral morphology into three types: crustal field aurora, non‐crustal field patchy aurora, and a new type we call “sinuous” aurora, an elongated serpentine structure that stretches thousands of kilometers into the nightside from near midnight in the northern hemisphere. These observations point to a highly dynamic environment in Mars' magnetotail.

Lillis, Robert J.↗
DOE OSTI2022

Episodes of Early Pleistocene West Antarctic Ice Sheet Retreat Recorded by Iceberg Alley Sediments

Abstract Ice loss in the Southern Hemisphere has been greatest over the past 30 years in West Antarctica. The high sensitivity of this region to climate change has motivated geologists to examine marine sedimentary records for evidence of past episodes of West Antarctic Ice Sheet (WAIS) instability. Sediments accumulating in the Scotia Sea are useful to examine for this purpose because they receive iceberg‐rafted debris (IBRD) sourced from the Pacific‐ and Atlantic‐facing sectors of West Antarctica. Here we report on the sedimentology and provenance of the oldest of three cm‐scale coarse‐grained layers recovered from this sea at International Ocean Discovery Program Site U1538. These layers are preserved in opal‐rich sediments deposited ∼1.2 Ma during a relatively warm regional climate. Our microCT‐based analysis of the layer's in‐situ fabric confirms its ice‐rafted origin. We further infer that it is the product of an intense but short‐lived episode of IBRD deposition. Based on the petrography of its sand fraction and the Phanerozoic 40 Ar/ 39 Ar ages of hornblende and mica it contains, we conclude that the IBRD it contains was likely sourced from the Weddell Sea and/or Amundsen Sea embayment(s) of West Antarctica. We attribute the high concentrations of IBRD in these layers to “dirty” icebergs calved from the WAIS following its retreat inland from its modern grounding line. These layers also sit at the top of a ∼366‐m thick Pliocene and early Pleistocene sequence that is much more dropstone‐rich than its overlying sediments. We speculate this fact may reflect that WAIS mass‐balance was highly dynamic during the ∼41‐kyr (inter)glacial world.

Bailey, Ian↗
DOE OSTI2026

Spectral Properties and Energy Injection in Mercury's Magnetotail Current Sheet

Mercury's magnetotail hosts a thin and highly dynamic current sheet (CS), where magnetic reconnection and strong fluctuations frequently occur. Here, we statistically analyze magnetic field power spectra across 370 magnetotail CSs observed by MESSENGER. About 20% of the events are quasi-laminar, showing single power-law spectra, whereas ∼80% are turbulent, exhibiting a spectral break separating inertial and kinetic ranges. A dawn–dusk asymmetry is identified: inertial-range slopes are systematically shallower on the dawnside, whereas kinetic-range slopes are steeper, indicating more developed turbulence there, consistent with the higher occurrence of reconnection-related processes on the dawnside. Component analysis shows that the transverse components, orthogonal to the tail-aligned principal field ( B X ), display shallow slopes near −1 in the inertial range, suggesting energy injection at ion scales rather than a classical inertial range. These results demonstrate that Mercury's unique plasma environment fundamentally reshapes the initiation of turbulence and the redistribution of energy in the magnetotail.

Mercury↗
DOE OSTI2025

Transition Zones at the Changing Coastal Terrestrial‐Aquatic Interface

Coastal soils are a significant but highly uncertain component of global biogeochemical cycles. These systems experience spatial and temporal variability in biogeochemical processes, driven by marsh‐to‐upland gradients and hydrological fluctuations. These fluctuations make it difficult to understand and predict biogeochemical processes in these highly dynamic systems. We studied coastal soil biogeochemistry and its variability (a) at regional scales and (b) across transects from upland forest to marsh, in two contrasting regions—Lake Erie, a freshwater lacustrine system, and Chesapeake Bay, a saltwater estuarine system. Salinity‐related analytes were a key source of variability in soil biogeochemistry, not just in the saltwater system, but surprisingly, also in the freshwater system. We had hypothesized linear trends in biogeochemical parameters along the TAI—however, contrary to expectations, transition soils were not consistently intermediate between upland and marsh endmembers; the non‐monotonic trends of C, P, Fe along our transects suggest that these do not behave as expected and may be difficult to model and predict—thus these are key analytes to study in our regions. Rapidly changing soil factors across coastal gradients (e.g., Ca, K, CEC, and TS) may act as precursors to ecosystem shifts. Our comprehensive soil characterization represents a snapshot of a single timepoint of surface soils and provides essential data for mechanistic modeling of ecosystem dynamics across coastal transects.

Patel, Kaizad F. [Pacific Northwest National Labor↗
DOE OSTI2026

Capturing Secondary Kinetic Instabilities in Three‐Dimensional Dayside Reconnection Using an Improved Gradient‐Based Closure

Magnetic reconnection is a highly dynamic process that excites a wide variety of kinetic waves and instabilities. Transverse current sheet instabilities such as the lower-hybrid drift and secondary drift-kink instabilities in particular have been shown by kinetic simulations to modify the reconnection and introduce significant turbulence and mixing to the reconnection layer. Past studies using the ten-moment fluid model to capture important kinetic physics such as the electron inertia and full representation of the pressure tensor proved advantageous to a two-fluid representation of reconnection, but the model struggled when using a local relaxation closure for the heat flux to replicate the current sheet instabilities and subsequent mixing seen in kinetic simulations. This work uses the Gkeyll software framework to perform simulations of asymmetric reconnection based on the 16 October 2015 MMS crossing of a diffusion region, the Burch event. An improved gradient-based heat flux closure is implemented, showing significant improvement in secondary kinetic instabilities that grow in the current sheet. These instabilities generate turbulence which leads to growth of secondary magnetic islands and flux ropes.

Bradshaw, K. [Princeton University, NJ (United Sta↗
DOE OSTI2024

Highly multiplexed design of an allosteric transcription factor to sense new ligands

Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures – four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone – as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

In-situ probing of the Fischer-Tropsch reaction on Co single crystal surfaces up to 1 bar

The surface chemistry of the Fischer-Tropsch catalytic reaction over Co has still several unknows. Here, we report an in-situ X-ray photoelectron spectroscopy study of Co$(0001)$ and Co$(10\bar{1}4)$, and in-situ high energy surface X-ray diffraction of Co$(0001)$ during the Fischer-Tropsch reaction at 0.15 bar - 1 bar and 406 K - 548 K in a H 2 /CO gas mixture. We find that these Co surfaces remain metallic under all conditions and that the coverage of chemisorbed species ranges from 0.4–1.7 monolayers depending on pressure and temperature. The adsorbates include CO on-top, C/-C x H y and various longer hydrocarbon molecules, indicating a rate-limiting direct CO dissociation pathway and that only hydrocarbon species participate in the chain growth. The accumulation of hydrocarbon species points to the termination step being rate-limiting also. Furthermore, we demonstrate that the intermediate surface species are highly dynamic, appearing and disappearing with time delays after rapid changes in the reactants’ composition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

NUB1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome

The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor NUB1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system with human components and revealed that NUB1 uses the intrinsic instability of FAT10 to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin-independent and p97-independent manner. Using hydrogen–deuterium exchange, structural modeling and site-directed mutagenesis, we identified the formation of an intricate complex with FAT10 that activates NUB1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic NUB1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These findings identified a previously unknown mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.

Arkinson, Connor↗
DOE OSTI2020

Phosphatidic acid: an emerging versatile class of cellular mediators

Abstract Lipids function not only as the major structural components of cell membranes, but also as molecular messengers that transduce signals to trigger downstream signaling events in the cell. Phosphatidic acid (PA), the simplest and a minor class of glycerophospholipids, is a key intermediate for the synthesis of membrane and storage lipids, and also plays important roles in mediating diverse cellular and physiological processes in eukaryotes ranging from microbes to mammals and higher plants. PA comprises different molecular species that can act differently, and is found in virtually all organisms, tissues, and organellar membranes, with variations in total content and molecular species composition. The cellular levels of PA are highly dynamic in response to stimuli and multiple enzymatic reactions can mediate its production and degradation. Moreover, its unique physicochemical properties compared with other glycerophospholipids allow PA to influence membrane structure and dynamics, and interact with various proteins. PA has emerged as a class of new lipid mediators modulating various signaling and cellular processes via its versatile effects, such as membrane tethering, conformational changes, and enzymatic activities of target proteins, and vesicular trafficking.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Comparing the shock sensitivity of insensitive energetic materials

We present a tabletop method to study the shock sensitivity of plastic-bonded explosives that are considered shock insensitive using high dynamic range optical emission spectroscopy with laser-launched km/s flyer plate impacts (2, 3, and 4 km/s), which measures the spectral radiance (the emission spectrum vs a calibrated intensity standard) every 0.8 ns in the nanosecond and microsecond regimes. The explosives were TATB (1,3,5 trinitro, 2,4,6 triamino benzene), FOX-7 (1,1-diamino-2,2-dinitroethylene), LLM-105 (2,6-diamino-3,5-dinitropyrazine-1-oxide), and NTO (nitrotriazolone), all with 20% Sylgard 182 binder. Time resolving emission from shocked explosives produces a unique fingerprint at each shock pressure, and the emission temporal profile can be used to understand each material's shock response and the underlying mechanisms within the framework of the well-known shock ignition and growth models. Ignition was characterized by the emission intensity during nanosecond hot spot ignition. The growth process, which occurs after the shock has unloaded, was characterized by the time derivative of microsecond emission intensity. Singular-value decomposition was used to determine a characteristic spectral radiance over the entire time range, and this radiance was fit to a graybody model to determine a characteristic temperature Tc. Even though these insensitive explosives have similar shock sensitivities, our method can clearly distinguish their shock response. FOX-7 and NTO were the most sensitive, with FOX-7 having the greatest shock ignition sensitivity, growth rate, and Tc. LLM-105 was much less sensitive than FOX-7 and NTO, and TATB consistently showed the lowest sensitivity by any measure.

Akhtar, Meysam (ORCID:0000000243897837)↗
DOE OSTI2025

Inference of the neutron down-scatter ratio using neutron time-of-flight data for DT-layered implosions on the OMEGA laser

First analysis of the neutron time of flight (nTOF) data is presented to infer the areal density using the neutron down-scatter ratio (DSR) for OMEGA deuterium–tritium (DT)-layered (cryogenic) implosions. The required very-high-dynamic range (nTOF) signal is constructed using an nTOF detector [Forrest et al., Rev. Sci. Ins. 83, 10D919 (2012)] with multiple time-gated photomultiplier tubes. The nTOF data are analyzed using a forward-fit technique to account for the detector responses and infer the DSR and areal density for DT-layered implosions. The areal densities inferred using this analysis are found to be in agreement with the areal densities measured using the magnetic recoil spectrometer detector that is located in a similar line-of-sight. This work establishes the feasibility of the DSR measurement using nTOF data on OMEGA and provides an additional areal-density measurement that will benefit the assessment of the implosion performance and 3D reconstruction of the imploded core.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection

In the indeterminate nodules of a model legume Medicago truncatula, ~700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea. In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enhanced chloroplast FtsZ-ring constriction by the ARC6–ARC3 module in Arabidopsis

Chloroplast division, a process tightly linked to the energy demands of plants, is initiated by the formation of the stromal filamenting temperature-sensitive Z (FtsZ) ring. The Z ring is highly dynamic, and its constriction provides the essential force for chloroplast division. However, the regulatory mechanisms governing Z-ring dynamics and constriction remain poorly understood. Here, we report that the chloroplast inner envelope membrane (IEM) protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS6 (ARC6) interacts with the chloroplast stromal protein ARC3, and this interaction is negatively regulated by the conserved J-like domain of ARC6. ARC3 is found both distributed throughout the stroma and localized to a ring-like structure at the chloroplast division site. We demonstrate that ARC6 recruits ARC3 to the division site to form a ring-like structure, likely through direct interaction. This ARC6–ARC3 interaction enables ARC3 to bind FtsZs. Furthermore, we show that the ARC6–ARC3 complex significantly promotes the dynamics of chloroplast Z rings reconstituted in a heterologous system. Finally, the constriction of these reconstituted Z rings is markedly enhanced by ARC6–ARC3. Our findings reveal a regulatory mechanism that governs Z-ring dynamics and constriction, shedding light on the molecular mechanisms underlying chloroplast division.

Science & Technology - Other Topics↗
DOE OSTI2020

More of the bulk from extremal area variations

It was shown recently in (Bao N et al 2019 Class. Quantum Grav. 36 185002), building on work of Alexakis, Balehowksy, and Nachman (Alexakis S et al 2017 arXiv:1711.09379), that the geometry of (some portion of) a manifold with boundary is uniquely fixed by the areas of a foliation of two-dimensional disk-shaped surfaces anchored to the boundary. In the context of AdS/CFT, this implies that (a portion of) a four-dimensional bulk geometry can be fixed uniquely from the entanglement entropies of disk-shaped boundary regions, subject to several constraints. Here, we loosen some of these constraints, in particular allowing for the bulk foliation of extremal surfaces to be local and removing the constraint of disk topology; these generalizations ensure uniqueness of more of the deep bulk geometry by allowing for e.g. surfaces anchored on disconnected asymptotic boundaries, or HRT surfaces past a phase transition. We also explore in more depth the generality of the local foliation requirement, showing that even in a highly dynamical geometry like AdS-Vaidya it is satisfied.

97 MATHEMATICS AND COMPUTING↗